singlem
Link to section 'Introduction' of 'singlem' Introduction
SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.
Docker hub: https://hub.docker.com/r/wwood/singlem
Home page: https://github.com/wwood/singlem
Link to section 'Versions' of 'singlem' Versions
- 0.13.2
Link to section 'Commands' of 'singlem' Commands
- singlem
Link to section 'Module' of 'singlem' Module
You can load the modules by:
module load biocontainers
module load singlem
Link to section 'Example job' of 'singlem' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run singlem on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=singlem
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers singlem